Publications

Theory of games and economic behavior

This is the classic work upon which modern-day game theory is based. What began more than sixty years ago as a modest proposal that a mathematician and an economist write a shor...

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction metho...

Cluster analysis and display of genome-wide expression patterns

A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according ...

Detecting Functionality-Specific Vulnerabilities via Retrieving Individual Functionality-Equivalent APIs in Open-Source Repositories

Functionality-specific vulnerabilities, which mainly occur in Application Programming Interfaces (APIs) with specific functionalities, are crucial for software developers to det...

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

Abstract Summary: RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies ...

Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift

Training Deep Neural Networks is complicated by the fact that the distribution of each layer's inputs changes during training, as the parameters of the previous layers change. T...

Qualitative research & evaluation methods

This book explains clearly conceptual issues and themes on qualitative research and evaluaton methods including: qualitative data, triangulated inquiry, qualitative inquiry, con...

UCHIME improves sensitivity and speed of chimera detection

Abstract Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Interna...

Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine

A two-dose regimen of BNT162b2 conferred 95% protection against Covid-19 in persons 16 years of age or older. Safety over a median of 2 months was similar to that of other viral...

Evolutionary trees from DNA sequences: A maximum likelihood approach

Numerical optimization

This third edition of Braun and Murdoch's bestselling textbook now includes discussion of the use and design principles of the tidyverse packages in R, including expanded covera...

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

The rapid development of high-throughput sequencing techniques has led biology into the big-data era. Data analyses using various bioinformatics tools rely on programming a...